I have to admit, the 3D effect was really good for me, and I adjusted to it immediately. I spend a good amount of time with it and didn't notice any eye strain, so I am pretty sure I'm going to get one now.
My co-worker, though he just had gotten new glasses had a horrible time with the 3d effect. It was hurting his eyes and he couldn't get the 3d effect at all. If you look at the screen from the side at all the picture completely goes crazy, the only way to view it is straight on.
One thing that I noticed that I really liked was the soft analog thumb pad thingie. I never tried a DSi, so I don't know if they have those, but its a nice feature on the 3ds.
Anyways, thats my update. Pilotwings was pretty fun too, I flew through some hoops, and the 3d effect added to the depth of being high in the sky.